Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP30850
DateWed Jan 25 15:20:48 GMT 2012
Unique Job ID8850cac2b6037c84

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2ix1A_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant
Confidence and coverage
Confidence:100.0% Coverage:100%
643 residues (100% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MFQDNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRI
Secondary structure 
SS confidence 
Disorder  ?????
??????
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  IAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNH
Secondary structure 
SS confidence 
Disorder 
??????
?????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  EFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVAT
Secondary structure 
SS confidence 
Disorder  ???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  EMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSK
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEF
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  FAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKD
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  RPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFD
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  PANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTE
Secondary structure 
SS confidence 
Disorder 
???
?
????????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  PGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRM
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  AERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDE
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640....
Sequence  LVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA
Secondary structure 
SS confidence 
Disorder 
?
?
??
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 2ix1 chain A

3D model

Region: 1 - 643
Aligned: 643
Modelled: 643
Confidence: 100.0%
Identity: 99%
PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant

Phyre2

PDB 2wp8 chain J

3D model

Region: 8 - 643
Aligned: 622
Modelled: 636
Confidence: 100.0%
Identity: 21%
PDB header:hydrolase
Chain: J: PDB Molecule:exosome complex exonuclease dis3;
PDBTitle: yeast rrp44 nuclease

Phyre2

PDB 2vnu chain D

3D model

Region: 2 - 634
Aligned: 615
Modelled: 630
Confidence: 100.0%
Identity: 20%
PDB header:hydrolase/rna
Chain: D: PDB Molecule:exosome complex exonuclease rrp44;
PDBTitle: crystal structure of sc rrp44

Phyre2

PDB 2r7f chain A

3D model

Region: 119 - 643
Aligned: 445
Modelled: 466
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease ii family protein;
PDBTitle: crystal structure of ribonuclease ii family protein from deinococcus2 radiodurans, hexagonal crystal form. northeast structural genomics3 target drr63

Phyre2

PDB 2ix0 chain A domain 4

3D model

Region: 173 - 557
Aligned: 385
Modelled: 385
Confidence: 100.0%
Identity: 100%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: RNB domain-like

Phyre2

PDB 2vnu chain D domain 4

3D model

Region: 160 - 556
Aligned: 390
Modelled: 397
Confidence: 100.0%
Identity: 24%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: RNB domain-like

Phyre2

PDB 2r7d chain A domain 2

3D model

Region: 119 - 557
Aligned: 386
Modelled: 394
Confidence: 100.0%
Identity: 25%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: RNB domain-like

Phyre2

PDB 2ix0 chain A domain 2

3D model

Region: 4 - 80
Aligned: 73
Modelled: 77
Confidence: 99.6%
Identity: 96%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2ix0 chain A domain 1

3D model

Region: 83 - 172
Aligned: 90
Modelled: 90
Confidence: 99.5%
Identity: 100%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2vnu chain D domain 3

3D model

Region: 8 - 82
Aligned: 74
Modelled: 75
Confidence: 99.3%
Identity: 18%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2vnu chain D domain 1

3D model

Region: 83 - 173
Aligned: 86
Modelled: 91
Confidence: 99.1%
Identity: 12%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2ix0 chain A domain 3

3D model

Region: 558 - 644
Aligned: 87
Modelled: 87
Confidence: 98.9%
Identity: 100%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1go3 chain E domain 1

3D model

Region: 557 - 640
Aligned: 77
Modelled: 84
Confidence: 98.9%
Identity: 16%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2c35 chain B domain 1

3D model

Region: 562 - 640
Aligned: 77
Modelled: 79
Confidence: 98.8%
Identity: 16%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 3h0g chain S

3D model

Region: 492 - 640
Aligned: 139
Modelled: 147
Confidence: 98.8%
Identity: 13%
PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe

Phyre2

PDB 1kl9 chain A domain 2

3D model

Region: 551 - 640
Aligned: 66
Modelled: 66
Confidence: 98.5%
Identity: 23%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2c35 chain F

3D model

Region: 557 - 640
Aligned: 80
Modelled: 84
Confidence: 98.5%
Identity: 16%
PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii

Phyre2

PDB 2k52 chain A

3D model

Region: 554 - 644
Aligned: 72
Modelled: 75
Confidence: 98.5%
Identity: 22%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein mj1198;
PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b

Phyre2

PDB 2b8k chain G

3D model

Region: 551 - 640
Aligned: 84
Modelled: 88
Confidence: 98.5%
Identity: 20%
PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii

Phyre2

PDB 1y14 chain B domain 1

3D model

Region: 562 - 640
Aligned: 70
Modelled: 77
Confidence: 98.5%
Identity: 23%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2
1
c2ix1A_
2
c2wp8J_
3
c2vnuD_
4
c2r7fA_
5
d2ix0a4
6
d2vnud4
7
d2r7da2
8
d2ix0a2
9
d2ix0a1
10
d2vnud3
11
d2vnud1
12
d2ix0a3
13
d1go3e1
14
d2c35b1
15
c3h0gS_
16
d1kl9a2
17
c2c35F_
18
c2k52A_
19
c2b8kG_
20
d1y14b1
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
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44
45
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2ix1A_
100.0 99 PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant
2c2wp8J_
100.0 21 PDB header:hydrolase
Chain: J: PDB Molecule:exosome complex exonuclease dis3;
PDBTitle: yeast rrp44 nuclease
3c2vnuD_
100.0 20 PDB header:hydrolase/rna
Chain: D: PDB Molecule:exosome complex exonuclease rrp44;
PDBTitle: crystal structure of sc rrp44
4c2r7fA_
100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease ii family protein;
PDBTitle: crystal structure of ribonuclease ii family protein from deinococcus2 radiodurans, hexagonal crystal form. northeast structural genomics3 target drr63
5d2ix0a4
100.0 100 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RNB domain-like
6d2vnud4
100.0 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RNB domain-like
7d2r7da2
100.0 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RNB domain-like
8d2ix0a2
99.6 96 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
9d2ix0a1
99.5 100 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
10d2vnud3
99.3 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
11d2vnud1
99.1 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
12d2ix0a3
98.9 100 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
13d1go3e1
98.9 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
14d2c35b1
98.8 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
15c3h0gS_
98.8 13 PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
16d1kl9a2
98.5 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
17c2c35F_
98.5 16 PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii
18c2k52A_
98.5 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein mj1198;
PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b
19c2b8kG_
98.5 20 PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii
20d1y14b1
98.5 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
21c1q46A_
not modelled 98.4 17 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia
22c1yz6A_
not modelled 98.4 19 PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 alpha
PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi
23d1q46a2
not modelled 98.3 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
24c1go3E_
not modelled 98.3 16 PDB header:transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex
25c2khiA_
not modelled 98.3 21 PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1
26c2cqoA_
not modelled 98.2 13 PDB header:ribosome
Chain: A: PDB Molecule:nucleolar protein of 40 kda;
PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067
27c1q8kA_
not modelled 98.2 19 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2
PDBTitle: solution structure of alpha subunit of human eif2
28c1nt9G_
not modelled 98.1 21 PDB header:transcription, transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kd polypeptide;
PDBTitle: complete 12-subunit rna polymerase ii
29c2k4kA_
not modelled 98.0 17 PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis
30c2ahoB_
not modelled 98.0 26 PDB header:translation
Chain: B: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: structure of the archaeal initiation factor eif2 alpha-2 gamma heterodimer from sulfolobus solfataricus complexed3 with gdpnp
31c2khjA_
not modelled 98.0 23 PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1
32d3bzka4
not modelled 98.0 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
33c1kl9A_
not modelled 98.0 27 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 subunit 1;
PDBTitle: crystal structure of the n-terminal segment of human eukaryotic2 initiation factor 2alpha
34c2pmzE_
not modelled 98.0 12 PDB header:translation, transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
35c3psiA_
not modelled 97.9 4 PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt6;
PDBTitle: crystal structure of the spt6 core domain from saccharomyces2 cerevisiae, form spt6(239-1451)
36c2eqsA_
not modelled 97.9 14 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dhx8;
PDBTitle: solution structure of the s1 rna binding domain of human2 atp-dependent rna helicase dhx8
37c2oceA_
not modelled 97.9 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa5201;
PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa
38d2ahob2
not modelled 97.9 26 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
39c2ckzB_
not modelled 97.8 9 PDB header:transferase
Chain: B: PDB Molecule:dna-directed rna polymerase iii 25 kd
PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25.
40d2vnud2
not modelled 97.8 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
41d2ba0a1
not modelled 97.8 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
42c3go5A_
not modelled 97.7 18 PDB header:gene regulation
Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains;
PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution
43d1sroa_
not modelled 97.7 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
44c1l2fA_
not modelled 97.6 18 PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain
45d2je6i1
not modelled 97.6 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
46d1wi5a_
not modelled 97.6 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
47d2z0sa1
not modelled 97.6 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
48d1hh2p1
not modelled 97.4 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
49c1hh2P_
not modelled 97.2 23 PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima
50d2nn6h1
not modelled 97.1 9 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
51d1g6pa_
not modelled 97.0 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
52d1a62a2
not modelled 96.9 29 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
53c2z0sA_
not modelled 96.8 18 PDB header:rna binding protein
Chain: A: PDB Molecule:probable exosome complex rna-binding protein 1;
PDBTitle: crystal structure of putative exosome complex rna-binding2 protein
54c2ytxA_
not modelled 96.6 28 PDB header:rna binding protein
Chain: A: PDB Molecule:cold shock domain-containing protein e1;
PDBTitle: solution structure of the second cold-shock domain of the human2 kiaa0885 protein (unr protein)
55c2k5nA_
not modelled 96.6 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative cold-shock protein;
PDBTitle: solution nmr structure of the n-terminal domain of protein2 eca1580 from erwinia carotovora, northeast structural3 genomics consortium target ewr156a
56c2a8vA_
not modelled 96.5 23 PDB header:protein/rna
Chain: A: PDB Molecule:rna binding domain of rho transcription
PDBTitle: rho transcription termination factor/rna complex
57d1smxa_
not modelled 96.5 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
58c3a0jB_
not modelled 96.4 25 PDB header:transcription
Chain: B: PDB Molecule:cold shock protein;
PDBTitle: crystal structure of cold shock protein 1 from thermus2 thermophilus hb8
59d1mjca_
not modelled 96.4 26 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
60c3aqqD_
not modelled 96.3 23 PDB header:dna binding protein
Chain: D: PDB Molecule:calcium-regulated heat stable protein 1;
PDBTitle: crystal structure of human crhsp-24
61c2kcmA_
not modelled 96.2 23 PDB header:nucleic acid binding protein
Chain: A: PDB Molecule:cold shock domain family protein;
PDBTitle: solution nmr structure of the n-terminal ob-domain of so_1732 from2 shewanella oneidensis. northeast structural genomics consortium3 target sor210a.
62d2nn6i1
not modelled 96.1 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
63c2ba0A_
not modelled 96.1 17 PDB header:rna binding protein
Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4;
PDBTitle: archaeal exosome core
64d2es2a1
not modelled 96.1 30 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
65d1h95a_
not modelled 96.1 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
66c3ayhB_
not modelled 96.0 20 PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase iii subunit rpc8;
PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii
67d1wfqa_
not modelled 95.9 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
68c3camB_
not modelled 95.7 25 PDB header:gene regulation
Chain: B: PDB Molecule:cold-shock domain family protein;
PDBTitle: crystal structure of the cold shock domain protein from neisseria2 meningitidis
69d1c9oa_
not modelled 95.6 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
70c1uwvA_
not modelled 95.6 17 PDB header:transferase
Chain: A: PDB Molecule:23s rrna (uracil-5-)-methyltransferase ruma;
PDBTitle: crystal structure of ruma, the iron-sulfur cluster2 containing e. coli 23s ribosomal rna 5-methyluridine3 methyltransferase
71c2rf4A_
not modelled 95.4 12 PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase i subunit rpa4;
PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43
72c2bh8B_
not modelled 95.3 21 PDB header:transcription
Chain: B: PDB Molecule:1b11;
PDBTitle: combinatorial protein 1b11
73c2nn6I_
not modelled 95.2 13 PDB header:hydrolase/transferase
Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
74d1uwva1
not modelled 95.1 14 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
75c2ytyA_
not modelled 94.9 22 PDB header:rna binding protein
Chain: A: PDB Molecule:cold shock domain-containing protein e1;
PDBTitle: solution structure of the fourth cold-shock domain of the human2 kiaa0885 protein (unr protein)
76c2je6I_
not modelled 94.8 18 PDB header:hydrolase
Chain: I: PDB Molecule:exosome complex rna-binding protein 1;
PDBTitle: structure of a 9-subunit archaeal exosome
77d1luza_
not modelled 94.7 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
78c3trzE_
not modelled 94.1 23 PDB header:rna binding protein/rna
Chain: E: PDB Molecule:protein lin-28 homolog a;
PDBTitle: mouse lin28a in complex with let-7d microrna pre-element
79c1xpuB_
not modelled 92.9 31 PDB header:transcription/rna
Chain: B: PDB Molecule:rho transcription termination factor;
PDBTitle: structural mechanism of inhibition of the rho transcription2 termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-3 dihydrobicyclomycin (fpdb)
80c2ba1B_
not modelled 92.3 16 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
81c1x65A_
not modelled 91.6 19 PDB header:rna binding protein
Chain: A: PDB Molecule:unr protein;
PDBTitle: solution structure of the third cold-shock domain of the human2 kiaa0885 protein (unr protein)
82c2vs1A_
not modelled 89.7 35 PDB header:transferase
Chain: A: PDB Molecule:uncharacterized rna methyltransferase pyrab10780;
PDBTitle: the crystal structure of pyrococcus abyssi trna (uracil-54,2 c5)-methyltransferase in complex with s-adenosyl-l-3 homocysteine
83d1yvca1
not modelled 89.4 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
84d1jjga_
not modelled 89.1 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
85d1jt8a_
not modelled 87.4 11 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
86d1yeza1
not modelled 84.4 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
87c2ytvA_
not modelled 84.0 20 PDB header:rna binding protein
Chain: A: PDB Molecule:cold shock domain-containing protein e1;
PDBTitle: solution structure of the fifth cold-shock domain of the human2 kiaa0885 protein (unr protein)
88c3i4oA_
not modelled 83.2 13 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor if-1;
PDBTitle: crystal structure of translation initiation factor 1 from2 mycobacterium tuberculosis
89c2oqkA_
not modelled 82.4 14 PDB header:translation
Chain: A: PDB Molecule:putative translation initiation factor eif-1a;
PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a
90d1u0la1
not modelled 81.9 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
91c2yv5A_
not modelled 81.3 17 PDB header:hydrolase
Chain: A: PDB Molecule:yjeq protein;
PDBTitle: crystal structure of yjeq from aquifex aeolicus
92d1ah9a_
not modelled 81.3 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
93c3l0oB_
not modelled 80.1 41 PDB header:hydrolase
Chain: B: PDB Molecule:transcription termination factor rho;
PDBTitle: structure of rna-free rho transcription termination factor from2 thermotoga maritima
94c2dgyA_
not modelled 69.6 19 PDB header:translation
Chain: A: PDB Molecule:mgc11102 protein;
PDBTitle: solution structure of the eukaryotic initiation factor 1a2 in mgc11102 protein
95d2nn6g1
not modelled 68.1 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
96c2i38A_
not modelled 67.1 16 PDB header:rna binding protein/chimera
Chain: A: PDB Molecule:fusion protein consists of immunoglobin g-
PDBTitle: solution structure of the rrm of srp20
97c2eqkA_
not modelled 65.0 17 PDB header:transcription
Chain: A: PDB Molecule:tudor domain-containing protein 4;
PDBTitle: solution structure of the tudor domain of tudor domain-2 containing protein 4
98d1hr0w_
not modelled 64.9 10 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
99c2rcnA_
not modelled 62.5 16 PDB header:hydrolase
Chain: A: PDB Molecule:probable gtpase engc;
PDBTitle: crystal structure of the ribosomal interacting gtpase yjeq from the2 enterobacterial species salmonella typhimurium.
100c2hqxB_
not modelled 61.9 14 PDB header:transcription
Chain: B: PDB Molecule:p100 co-activator tudor domain;
PDBTitle: crystal structure of human p100 tudor domain conserved2 region
101d2hqxa1
not modelled 61.9 14 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
102c3d0fA_
not modelled 60.1 21 PDB header:transferase
Chain: A: PDB Molecule:penicillin-binding 1 transmembrane protein mrca;
PDBTitle: structure of the big_1156.2 domain of putative penicillin-binding2 protein mrca from nitrosomonas europaea atcc 19718
103c1k0rB_
not modelled 59.3 24 PDB header:transcription
Chain: B: PDB Molecule:nusa;
PDBTitle: crystal structure of mycobacterium tuberculosis nusa
104d1t9ha1
not modelled 59.3 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
105d1f39a_
not modelled 56.6 12 Fold:LexA/Signal peptidase
Superfamily:LexA/Signal peptidase
Family:LexA-related
106c2wacA_
not modelled 52.7 17 PDB header:splicing
Chain: A: PDB Molecule:cg7008-pa;
PDBTitle: extended tudor domain of drosophila melanogaster tudor-sn (2 p100)
107c4a4fA_
not modelled 51.0 22 PDB header:rna binding protein
Chain: A: PDB Molecule:survival of motor neuron-related-splicing factor 30;
PDBTitle: solution structure of spf30 tudor domain in complex with2 symmetrically dimethylated arginine
108d1e3pa2
not modelled 50.4 31 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
109d1mhna_
not modelled 49.0 17 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
110c2xnqA_
not modelled 49.0 16 PDB header:rna binding protein
Chain: A: PDB Molecule:nuclear polyadenylated rna-binding protein 3;
PDBTitle: structural insights into cis element recognition of non-2 polyadenylated rnas by the nab3-rrm
111d2diqa1
not modelled 48.9 20 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
112c3metB_
not modelled 48.5 13 PDB header:transcription
Chain: B: PDB Molecule:saga-associated factor 29 homolog;
PDBTitle: crystal structure of sgf29 in complex with h3k4me2
113d1d7qa_
not modelled 48.0 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
114c2d9tA_
not modelled 43.7 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:tudor domain-containing protein 3;
PDBTitle: solution structure of the tudor domain of tudor domain2 containing protein 3 from mouse
115c2c4rL_
not modelled 43.0 18 PDB header:hydrolase
Chain: L: PDB Molecule:ribonuclease e;
PDBTitle: catalytic domain of e. coli rnase e
116c3pnwX_
not modelled 42.8 17 PDB header:protein binding/immune system
Chain: X: PDB Molecule:tudor domain-containing protein 3;
PDBTitle: crystal structure of the tudor domain of human tdrd3 in complex with2 an anti-tdrd3 fab
117c1g5vA_
not modelled 38.4 17 PDB header:translation
Chain: A: PDB Molecule:survival motor neuron protein 1;
PDBTitle: solution structure of the tudor domain of the human smn2 protein
118d2ja9a1
not modelled 37.3 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
119d2cqda1
not modelled 36.9 14 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
120d2asba1
not modelled 35.8 27 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite


Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
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Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0